LYTH - BACSU - GREMLIN Contacts

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LYTH - L-Ala--D-Glu endopeptidase

UniProt:	O32130	Sequences: MKVLLSALLLLLFAFEPSASGKKLSDPVLSKRMELYHKIEAVTQIPWYALAAVDQYEENVRSNRKDLPEKAGIISIYIPDDIWSGPENPNPKDDAPLSIKVFDGIGMDGDGDGKAEVSNDEDILYTFSQYLLSYGTDEDNIRIGLWNYYRRDQTVGIISEFMKLFKAYGHIDLGEHAFPLPIRTDYSYRSTWGDARGFGGRRIHEGTDIFAHYGLPVKSTCYGVVEMKGWNRFGGWRIGIRDINNTYHYFAHLNGFAKGIKTGQIVEPGQVIGSVGSSGYGPPGTAGKFPPHLHYGMYKDNGRTEWSFDPYPHLRAWERYEYQKKK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	326 (282)
Sequences:	3500 (3166)
Seq/√Len:	188.5

ECOLI - MEPM ENVC NLPD YGER
BACSU - LYTH SP4FA SP2Q

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
253_L	273_G	3.816	1.00
242_D	248_H	3.110	1.00
228_K	256_F	3.108	1.00
217_V	253_L	3.095	1.00
189_R	210_F	2.945	1.00
211_A	275_V	2.814	1.00
277_S	288_K	2.769	1.00
191_T	311_Y	2.720	1.00
257_A	274_S	2.675	1.00
216_P	271_V	2.616	1.00
192_W	307_S	2.597	1.00
180_L	209_I	2.495	1.00
213_Y	291_P	2.481	1.00
179_P	268_P	2.350	1.00
222_Y	267_E	2.289	1.00
219_S	240_I	2.135	1.00
220_T	295_Y	2.062	1.00
234_G	251_A	2.043	1.00
145_L	149_Y	1.979	1.00
138_E	142_R	1.953	1.00
103_D	107_M	1.915	1.00
253_L	256_F	1.879	1.00
220_T	248_H	1.846	1.00
224_V	265_I	1.803	1.00
187_S	210_F	1.800	1.00
190_S	195_A	1.795	1.00
197_G	202_R	1.783	1.00
109_G	112_D	1.773	1.00
140_N	144_G	1.760	1.00
151_R	154_T	1.752	1.00
260_I	264_Q	1.746	1.00
186_Y	209_I	1.733	1.00
126_T	130_Y	1.732	1.00
127_F	131_L	1.731	1.00
110_D	114_K	1.727	1.00
248_H	297_M	1.719	1.00
149_Y	153_Q	1.714	1.00
141_I	145_L	1.709	1.00
251_A	296_G	1.688	1.00
147_N	151_R	1.685	1.00
205_E	296_G	1.677	1.00
208_D	294_H	1.653	1.00
117_V	121_E	1.596	1.00
133_S	137_D	1.592	1.00
142_R	146_W	1.587	1.00
267_E	270_Q	1.552	1.00
96_P	100_K	1.544	1.00
217_V	275_V	1.543	1.00
240_I	272_I	1.542	1.00
152_D	155_V	1.525	1.00
67_L	74_I	1.514	1.00
194_D	203_I	1.504	1.00
146_W	150_R	1.479	1.00
271_V	274_S	1.468	1.00
197_G	200_G	1.458	1.00
137_D	140_N	1.445	1.00
95_A	98_S	1.439	1.00
239_G	249_Y	1.436	1.00
132_L	136_T	1.431	1.00
102_F	105_I	1.431	1.00
150_R	154_T	1.420	1.00
25_S	29_L	1.406	1.00
106_G	110_D	1.397	1.00
85_G	89_P	1.397	1.00
218_K	271_V	1.353	1.00
130_Y	133_S	1.352	1.00
86_P	89_P	1.349	1.00
116_E	119_N	1.346	1.00
134_Y	137_D	1.343	1.00
220_T	250_F	1.339	1.00
123_I	126_T	1.336	1.00
105_I	109_G	1.333	1.00
144_G	147_N	1.326	1.00
238_I	272_I	1.312	1.00
183_R	218_K	1.303	1.00
180_L	186_Y	1.296	1.00
124_L	128_S	1.295	1.00
204_H	208_D	1.291	1.00
239_G	247_Y	1.283	1.00
151_R	155_V	1.265	1.00
143_I	147_N	1.259	1.00
208_D	292_H	1.258	1.00
221_C	268_P	1.254	1.00
238_I	253_L	1.253	1.00
134_Y	138_E	1.250	1.00
157_I	161_F	1.248	1.00
101_V	105_I	1.246	1.00
246_T	299_K	1.242	1.00
146_W	149_Y	1.241	1.00
104_G	107_M	1.239	1.00
226_E	241_R	1.238	1.00
260_I	270_Q	1.226	1.00
211_A	215_L	1.225	1.00
119_N	123_I	1.218	1.00
275_V	293_L	1.215	1.00
139_D	142_R	1.214	1.00
120_D	124_L	1.210	1.00
135_G	139_D	1.184	1.00
261_K	264_Q	1.175	1.00
190_S	204_H	1.170	1.00
63_N	66_D	1.169	1.00
112_D	115_A	1.166	1.00
148_Y	152_D	1.166	1.00
113_G	117_V	1.165	1.00
21_G	24_L	1.164	1.00
226_E	247_Y	1.157	1.00
21_G	25_S	1.156	1.00
92_K	96_P	1.146	1.00
309_D	312_P	1.146	1.00
49_A	52_A	1.141	1.00
125_Y	129_Q	1.131	1.00
107_M	111_G	1.129	1.00
70_K	74_I	1.126	1.00
70_K	73_I	1.125	1.00
255_G	274_S	1.122	1.00
137_D	141_I	1.119	1.00
62_S	66_D	1.119	1.00
81_D	88_N	1.115	1.00
24_L	27_P	1.114	1.00
93_D	97_L	1.109	1.00
157_I	160_E	1.107	1.00
19_A	22_K	1.107	1.00
233_F	251_A	1.104	1.00
100_K	103_D	1.100	1.00
108_D	112_D	1.097	1.00
156_G	159_S	1.095	1.00
275_V	291_P	1.091	1.00
208_D	252_H	1.090	1.00
120_D	123_I	1.090	1.00
40_E	43_T	1.089	1.00
77_Y	80_D	1.085	1.00
142_R	145_L	1.083	1.00
100_K	104_G	1.075	1.00
141_I	144_G	1.073	1.00
55_Q	59_N	1.072	1.00
234_G	296_G	1.071	1.00
139_D	143_I	1.068	1.00
231_N	237_R	1.066	1.00
207_T	311_Y	1.065	1.00
128_S	131_L	1.061	1.00
236_W	278_S	1.060	1.00
18_S	22_K	1.055	1.00
148_Y	151_R	1.051	1.00
204_H	292_H	1.050	1.00
298_Y	307_S	1.050	1.00
182_I	186_Y	1.047	1.00
84_S	87_E	1.047	1.00
213_Y	254_N	1.047	1.00
227_M	239_G	1.045	1.00
81_D	84_S	1.045	1.00
66_D	70_K	1.043	1.00
224_V	241_R	1.039	1.00
114_K	117_V	1.029	1.00
73_I	77_Y	1.021	1.00
161_F	165_F	1.019	1.00
78_I	82_I	1.018	1.00
257_A	271_V	1.016	1.00
196_R	199_G	1.014	1.00
160_E	163_K	1.009	1.00
144_G	148_Y	1.008	1.00
150_R	153_Q	1.006	1.00
158_I	162_M	1.005	1.00
147_N	150_R	1.004	0.99
106_G	109_G	1.004	0.99
207_T	314_L	1.001	0.99
45_I	49_A	1.000	0.99
90_N	94_D	0.997	0.99
145_L	148_Y	0.997	0.99
39_I	43_T	0.996	0.99
154_T	157_I	0.994	0.99
81_D	85_G	0.992	0.99
152_D	156_G	0.990	0.99
64_R	68_P	0.988	0.99
135_G	138_E	0.987	0.99
127_F	130_Y	0.985	0.99
74_I	78_I	0.980	0.99
98_S	102_F	0.979	0.99
252_H	279_G	0.974	0.99
102_F	106_G	0.974	0.99
82_I	85_G	0.972	0.99
68_P	71_A	0.972	0.99
118_S	122_D	0.971	0.99
50_L	54_D	0.963	0.99
112_D	116_E	0.963	0.99
138_E	145_L	0.961	0.99
215_L	275_V	0.954	0.99
183_R	186_Y	0.952	0.99
63_N	67_L	0.951	0.99
36_Y	40_E	0.949	0.99
237_R	251_A	0.944	0.99
161_F	164_L	0.937	0.99
122_D	126_T	0.935	0.99
103_D	106_G	0.934	0.99
277_S	291_P	0.932	0.99
109_G	113_G	0.929	0.99
222_Y	268_P	0.926	0.99
230_W	236_W	0.924	0.99
246_T	297_M	0.924	0.99
257_A	273_G	0.918	0.99
83_W	87_E	0.915	0.99
114_K	118_S	0.911	0.99
31_K	34_E	0.903	0.99
84_S	88_N	0.895	0.99
119_N	122_D	0.893	0.99
212_H	215_L	0.892	0.99
132_L	135_G	0.890	0.99
234_G	249_Y	0.884	0.99
52_A	55_Q	0.879	0.99
196_R	201_R	0.878	0.99
149_Y	152_D	0.877	0.99
296_G	307_S	0.876	0.99
32_R	36_Y	0.874	0.99
237_R	249_Y	0.871	0.99
56_Y	59_N	0.869	0.99
77_Y	81_D	0.866	0.99
99_I	103_D	0.865	0.98
52_A	56_Y	0.863	0.98
73_I	76_I	0.859	0.98
61_R	64_R	0.858	0.98
72_G	75_S	0.858	0.98
159_S	162_M	0.858	0.98
154_T	158_I	0.856	0.98
116_E	120_D	0.854	0.98
191_T	309_D	0.850	0.98
194_D	197_G	0.845	0.98
117_V	120_D	0.845	0.98
125_Y	128_S	0.844	0.98
158_I	161_F	0.844	0.98
234_G	298_Y	0.842	0.98
75_S	78_I	0.837	0.98
277_S	289_F	0.832	0.98
159_S	163_K	0.832	0.98
121_E	125_Y	0.831	0.98
48_Y	52_A	0.831	0.98
98_S	101_V	0.830	0.98
29_L	33_M	0.828	0.98
94_D	98_S	0.826	0.98
60_V	64_R	0.818	0.98
74_I	77_Y	0.818	0.98
46_P	50_L	0.817	0.98
251_A	298_Y	0.804	0.98
136_T	140_N	0.804	0.98
216_P	274_S	0.797	0.97
42_V	45_I	0.795	0.97
138_E	141_I	0.793	0.97
131_L	135_G	0.791	0.97
69_E	73_I	0.791	0.97
107_M	110_D	0.779	0.97
130_Y	134_Y	0.778	0.97
209_I	314_L	0.778	0.97
230_W	278_S	0.774	0.97
49_A	53_V	0.766	0.97
242_D	250_F	0.766	0.97
180_L	183_R	0.762	0.97
220_T	297_M	0.760	0.97
246_T	313_H	0.759	0.97
59_N	63_N	0.759	0.97
189_R	290_P	0.758	0.97
37_H	41_A	0.755	0.96
38_K	41_A	0.754	0.96
250_F	295_Y	0.752	0.96
118_S	121_E	0.751	0.96
41_A	45_I	0.749	0.96
27_P	30_S	0.747	0.96
61_R	65_K	0.745	0.96
43_T	47_W	0.742	0.96
19_A	23_K	0.742	0.96
111_G	114_K	0.738	0.96
302_G	307_S	0.733	0.96
140_N	143_I	0.731	0.96
186_Y	210_F	0.730	0.96
242_D	295_Y	0.727	0.96
126_T	129_Q	0.724	0.96
57_E	61_R	0.723	0.95
205_E	307_S	0.723	0.95
99_I	102_F	0.723	0.95
237_R	253_L	0.722	0.95
197_G	201_R	0.722	0.95
254_N	274_S	0.716	0.95
93_D	96_P	0.715	0.95
95_A	99_I	0.715	0.95
22_K	25_S	0.713	0.95
34_E	38_K	0.710	0.95
238_I	260_I	0.709	0.95
18_S	21_G	0.704	0.95
104_G	108_D	0.703	0.95
182_I	211_A	0.701	0.95
113_G	116_E	0.699	0.95
180_L	314_L	0.699	0.95
248_H	295_Y	0.693	0.94
188_Y	311_Y	0.693	0.94
85_G	88_N	0.690	0.94
160_E	164_L	0.685	0.94
92_K	95_A	0.683	0.94
225_V	260_I	0.682	0.94
76_I	80_D	0.680	0.94
252_H	297_M	0.679	0.94
153_Q	157_I	0.678	0.94
227_M	237_R	0.677	0.94
71_A	75_S	0.676	0.94
115_A	119_N	0.674	0.93
54_D	57_E	0.671	0.93
156_G	160_E	0.669	0.93
253_L	275_V	0.669	0.93
59_N	62_S	0.666	0.93
223_G	240_I	0.666	0.93
24_L	28_V	0.664	0.93
38_K	42_V	0.661	0.93
227_M	231_N	0.660	0.93
35_L	39_I	0.658	0.93
127_F	134_Y	0.657	0.93
18_S	25_S	0.656	0.93
42_V	46_P	0.652	0.92
75_S	79_P	0.652	0.92
249_Y	298_Y	0.649	0.92
308_F	313_H	0.647	0.92
72_G	76_I	0.645	0.92
210_F	290_P	0.645	0.92
253_L	257_A	0.639	0.92
127_F	152_D	0.639	0.92
40_E	44_Q	0.639	0.92
27_P	31_K	0.637	0.91
20_S	24_L	0.636	0.91
235_G	276_G	0.636	0.91
231_N	239_G	0.634	0.91
66_D	69_E	0.633	0.91
252_H	288_K	0.630	0.91
189_R	288_K	0.630	0.91
109_G	116_E	0.630	0.91
239_G	298_Y	0.627	0.91
123_I	127_F	0.625	0.91
234_G	237_R	0.623	0.91
178_F	246_T	0.621	0.90
47_W	51_A	0.619	0.90
188_Y	207_T	0.619	0.90
194_D	202_R	0.618	0.90
197_G	205_E	0.616	0.90
276_G	292_H	0.613	0.90
171_I	174_G	0.611	0.90
171_I	175_E	0.610	0.90
252_H	292_H	0.610	0.90
189_R	292_H	0.608	0.89
254_N	257_A	0.607	0.89
45_I	48_Y	0.605	0.89
120_D	134_Y	0.605	0.89
299_K	308_F	0.602	0.89
175_E	221_C	0.601	0.89
204_H	290_P	0.599	0.89
80_D	84_S	0.597	0.89
190_S	208_D	0.597	0.89
102_F	120_D	0.596	0.88
179_P	220_T	0.595	0.88
105_I	108_D	0.595	0.88
90_N	93_D	0.594	0.88
131_L	137_D	0.593	0.88
241_R	301_N	0.592	0.88
162_M	165_F	0.592	0.88
145_L	152_D	0.590	0.88
178_F	313_H	0.589	0.88
56_Y	60_V	0.589	0.88
102_F	127_F	0.585	0.88
188_Y	191_T	0.580	0.87
208_D	279_G	0.578	0.87
181_P	242_D	0.577	0.87
53_V	74_I	0.576	0.87
77_Y	84_S	0.576	0.87
148_Y	155_V	0.574	0.87
118_S	126_T	0.572	0.86
278_S	287_G	0.571	0.86
211_A	214_G	0.569	0.86
204_H	294_H	0.569	0.86
243_I	300_D	0.568	0.86
273_G	293_L	0.567	0.86
128_S	132_L	0.566	0.86
28_V	32_R	0.565	0.86
131_L	134_Y	0.565	0.86
174_G	221_C	0.563	0.86
51_A	55_Q	0.561	0.85
120_D	127_F	0.560	0.85
91_P	95_A	0.559	0.85
134_Y	145_L	0.559	0.85
207_T	310_P	0.557	0.85
311_Y	314_L	0.556	0.85
53_V	56_Y	0.555	0.85
208_D	290_P	0.554	0.85
192_W	308_F	0.551	0.84
252_H	278_S	0.549	0.84
204_H	252_H	0.549	0.84
253_L	293_L	0.548	0.84
91_P	94_D	0.547	0.84
230_W	233_F	0.543	0.83
217_V	293_L	0.543	0.83
178_F	221_C	0.541	0.83
234_G	239_G	0.537	0.83
171_I	178_F	0.536	0.83
33_M	36_Y	0.533	0.82
42_V	88_N	0.533	0.82
241_R	247_Y	0.531	0.82
134_Y	142_R	0.531	0.82
67_L	70_K	0.529	0.82
249_Y	296_G	0.528	0.82
102_F	109_G	0.527	0.82
28_V	31_K	0.524	0.81
247_Y	300_D	0.522	0.81
189_R	204_H	0.522	0.81
58_E	62_S	0.521	0.81
252_H	294_H	0.521	0.81
193_G	203_I	0.521	0.81
97_L	101_V	0.520	0.81
241_R	298_Y	0.518	0.81
214_G	254_N	0.518	0.81
120_D	128_S	0.518	0.81
143_I	146_W	0.513	0.80
218_K	269_G	0.513	0.80
252_H	276_G	0.512	0.80
84_S	89_P	0.511	0.80
175_E	315_R	0.510	0.80
194_D	201_R	0.510	0.80
129_Q	133_S	0.503	0.79
82_I	86_P	0.503	0.79
252_H	290_P	0.503	0.79
214_G	275_V	0.501	0.78
26_D	29_L	0.500	0.78

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Prob ≥ 0.7 are listed. For all 3L/2 predictions, click on one of the links below.

Sco = ((raw_sco - min_sco)/(avg_sco - min_sco))/2 + 0.5
Prob = P(contact | Sco, seq80/√len)
seq80 = effective number of sequences, after reducing redundancy to 80% identity

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling
Upload PDB model overlay contacts on the model

HHsearch Results:

Legend: GREMLIN results (Prob ≥ 0.7) overlaid on top PDB hits. The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on the top 10 (or top 20 if e-value < 1E-20) HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.

PDB	Chains	Cov	%	HHΔ
4bh5A	4	0.3988	100	0.455	Contact Map
2hsiA	1	0.5644	100	0.47	Contact Map
3tufB	1	0.4233	100	0.474	Contact Map
4rnzA	1	0.8957	100	0.481	Contact Map
2gu1A	1	0.8896	100	0.498	Contact Map
1qwyA	1	0.5215	100	0.501	Contact Map
3sluA	1	0.9417	100	0.509	Contact Map
3nyyA	2	0.7025	100	0.509	Contact Map
4qp5A	1	0.4049	100	0.516	Contact Map
4lxcA	4	0.4387	100	0.523	Contact Map

Sequence Conservation (Image Generated using WebLogo v3)

Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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